Dear Olivier, We plan to add toxoplasma, using gene calls from toxo db, in the next release of ensembl protists (due 6th march), whereupon this data will become available in the ensembl protists biomart.
Best wishes, Paul Sent from my iPhone On 22 Jan 2012, at 02:20, Arek Kasprzyk <[email protected]> wrote: > > > On Sat, Jan 21, 2012 at 7:08 PM, Arek Kasprzyk <[email protected]> > wrote: > > On Sat, Jan 21, 2012 at 10:51 AM, Olivier Lucas <[email protected]> wrote: > Dear Arek, > > I am a postdoc in Molecular Medicine at the University of South Florida. I > am an experimental biologist turning to a more computational approach (and > also looking for a job in that realm). I study gene regulation in Toxoplasma > gondii (protist). This organism, along with Plasmodium and other protists > has a great gene-centric database (toxodb.org and eupathdb.org for Plasmodium > and other protists) and a vibrant community. All the data is publicly > available and queryable through their non-user friendly webservices. > > Unfortunately it is not hosted through Biomart. I have contacted the > developers and maintainers of toxoDB and the small team is too swamped > creating a great user interface and compiling data (which they do an awesome > job at) to have time to make it compatible with biomart. Thus, data mining in > those organisms is very limited. I was wondering if there would be any > interest on your side and/or what would be the logistics (and politics) > involved. To me it does not make sens not to have such great public data not > available to a broader community. I'd love to do something about it! > > Regardless, biomart is one of the most fantastic resource out there. Keep up > the good work!! > > Sincerely, > > -- > Olivier > > > Hi Olivier, > I agree with you that toxodb and europah are fantastic resources. The BioMart > project is a software development project and all our services are provided > from the independently and remotely maintained resources. We do not host any > data ourselves. However I suspect that there are people on this list who may > have some experience in 'martifying' similar resources and perhaps would be > able to provide some advice for you or someone else who would be willing to > try to create a biomart based on these data. For instance there is an Ensembl > resource dedicated to protists available from Ensembl and described in this > paper: > > http://database.oxfordjournals.org/content/2011/bar030.full > > I am also cc'ing Paul and Rhoda who would be able to give you more pointers. > I also hope that somebody else from this list may chip in with more > information > > sorry, now i am really cc'ing Paul and Rhoda :) > > a > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead >
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